[gmx-users] Re: RDF output has no data

[Dr. Vitaly Chaban]

I believe the problem is in the way which you used to convert AMBER
trajectory to the GROMACS trajectory....

I would suggest to try gmxdump and see what your trajectory looks like. Oe
maybe even better - try to visualize it in VMD to see if the format is
correct.

Dr. Vitaly Chaban



Sir
>
> I was using an old version. Now I used 4.5.5, it still gives me the same
> blank output file.
>
> Kindly suggest how to go about solving this
>
> Thanks
>
>
> On Sat, Apr 6, 2013 at 2:26 PM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
>
> > On Sat, Apr 6, 2013 at 7:19 AM, Venkat Reddy <venkat4bt at gmail.com>
> wrote:
> >
> > > There was no fatal error preceding the output. After selecting the
> groups
> > > following are the output on the screen
> > > Reading frame       1 time    0.100
> > > Warning: can not make broken molecules whole without a run input file,
> > >          don't worry, mdrun doesn't write broken molecules
> > >
> >
> > This message is from a prehistoric version of g_rdf. Please get a new
> one.
> >
> > Mark
> >
> >
> > >
> > > Reading frame    2000 time  200.000
> > >
> > >
> > > gcq#69: "The Wheels On the Bus Go Round and Round" (J. Richman)
> > >
> > > And the rdf.xvg file looks like this
> > >
> > > #This file was created Sat Apr  6 10:54:13 2013
> > > # by the following command:
> > > # g_rdf -f 6md.trr -s ../../6md.pdb -n rdf.ndx -o rdf.xvg
> > > #
> > > # g_rdf is part of G R O M A C S:
> > > #
> > > # GROningen MAchine for Chemical Simulation
> > > #
> > > @    title "Radial Distribution"
> > > @    xaxis  label "r"
> > > @    yaxis  label ""
> > > @TYPE xy
> > > @ subtitle "O21-H2_&_CAT"
> > >      0.001          1
> > > ~
> > >
> > > Whats going wrong? Please help.
>